On Saturday, 19 January 2013, Luecke, Hartmut wrote:
>
> In recent CASPs, there has been a shortage of new folds (according to PDB
> exactly zero new folds deposited since 2009) and membrane protein targets.
I have been wondering about that. It is true that the PDB has not listed any
"new folds" since 2009, but that hasn't stopped people from publishing new
structures and claiming they are new folds. Is this because there is no
single recognized criterion for "new" in these cases?
Or possibly the PDB hasn't updated their statistics since 2009?
E.g. from the 1st page of Google Scholar hits for "protein structure new fold"
2RSX R Arai, S Fukui, N Kobayashi, J Sekiguchi - JBC 2012
Solution Structure of IseA, an Inhibitor Protein of
dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold
3RX6 R Banerjee, S Nath, A Ranjan, S Khamrui, B Pani, R Sen, U Sen -
JBC 2012
"A search of the Protein Data Bank using the DALI server (19)
and PDBeFold (20) did not produce any significant match with
the Psu structure designating it to be a new fold"
2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011
Structure and genetic analysis of the arterivirus nonstructural
protein 7α
Ethan Merritt
> The lack of such targets makes it problematic to reliably quantify the state
> of the art in the area of protein structure prediction. To remedy this
> situation, CASP organizers have recently launched a new project called CASP
> ROLL (http://predictioncenter.org/casprol), where amino acids sequences of
> challenging targets are released throughout the year when structure solution
> is imminent. CASP specifically needs sequences of low-homology membrane
> targets that are about to be solved or have been solved but not released by
> PDB or elsewhere yet. It is important that structural information about the
> targets has not been publicly exposed (including things like coordinates,
> images, papers, conference abstracts) until after the prediction window for
> a given target has been closed.
>
> Each target will be available for prediction for a period of three to four
> weeks; in some cases a longer "hold" (up to 8 weeks) may be requested to
> allow the same target to be re-used for additional modeling experiments.
>
> So if you have anything suitable - please let CASP know. As you saw from the
> information above, your targets need not be fully refined structures. And if
> you need to make public a target's structure before the CASP window closes,
> simply contact CASP. We would rather lose a few targets than not have any
> at all!
>
> A good perspective for solving the structure in a few months is a good
> enough assurance for CASP. The submission mechanism is really simple. You
> can submit a target using the CASP Target Submission Form
> (http://predictioncenter.org/casprol/targets_submission.cgi), by sending
> email to c...@predictioncenter.org, or by marking your PDB deposition as
> "CASP target" in PDB's ADIT system (this way PDB will automatically put your
> target "on hold for CASP for 8 weeks").
>
> Submission details can be found at
> http://predictioncenter.org/casprol/targets_submission.cgi
>
> Thanks and hoping for lots of targets.
>
>
> Hudel, UC Irvine
>
>
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